title: TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.
abstract: BACKGROUND
  Many human genes express multiple transcript isoforms through alternative splicing, which greatly increases diversity of protein function. Although RNA sequencing (RNA-Seq) technologies have been widely used in measuring amounts of transcribed mRNA, accurate estimation of transcript isoform abundances from RNA-Seq data is challenging because reads often map to more than one transcript isoforms or paralogs whose sequences are similar to each other.
  
  
  RESULTS
  We propose a statistical method to estimate transcript isoform abundances from RNA-Seq data. Our method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads. The proposed method optimizes the number of transcript isoforms by variational Bayesian inference through an iterative procedure, and its convergence is guaranteed under a stopping criterion. On simulated datasets, our method outperformed the comparable quantification methods in inferring transcript isoform abundances, and at the same time its rate of convergence was faster than that of the expectation maximization algorithm. We also applied our method to RNA-Seq data of human cell line samples, and showed that our prediction result was more consistent among technical replicates than those of other methods.
  
  
  BACKGROUND
  An implementation of our method is available at http://github.com/nariai/tigar
  
  
  BACKGROUND
  nariai@megabank.tohoku.ac.jp
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan. nariai@megabank.tohoku.ac.jp
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.forename: Osamu
authors.initials: O
authors.lastname: Hirose
authors.forename: Kaname
authors.initials: K
authors.lastname: Kojima
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D001499:Bayes Theorem; D002460:Cell Line; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D059368:RNA Isoforms / Q000032:analysis* / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D059368:RNA Isoforms